Multi-Well Tools

Tools to extract data produced by multi-well microscope experiments i.e. Nautilus

Run the script from the command line

> python /path/to/well_data.py /path/to/json_config --input_video_path /path/to/input/video --output_dir_path /path/to/output/dir

args with a leading -- are optional and if supplied will override keys with the same name in the json config.

Basic System Test

To run a basic system test, if you are in the main directory (multiwell_tools) :

python ./src/well_data.py "./test_data/CuriBio 24 Well Plate.json" --input_video_path .\test_data\default__2023_04_21_231442.raw --output_dir_path .\test_data\default__2023_04_21_231442Results --num_horizontal_pixels 1536 --num_vertical_pixels 1024 --num_frames 20 --bit_depth 16 --scale_factor 2 --duration 1 --fps 20

This will run the well data extraction function which will produce:

• xlsx files with the time series data from each well,
• a zip archive of all the xlsx files,
• an image with the roi's drawn on one frame of the input video,
• a plot of every wells time series data.